A reaction in which daughter DNAs are synthesized using the parental DNAs as the template. Transferring the genetic information to the descendant generation with a high fidelity Semi-conservative replication Bidirectional replication Semi-continuous replication High fidelity Replication starts from unwinding the dsDNA at a particular point (called origin), followed by the synthesis on each strand. The parental dsDNA and two newly formed dsDNA form a Y-shape structure called replication fork.

1. Section 1
General Concepts of
DNA Replication

2. DNA replication
• A reaction in which daughter DNAs are
synthesized using the parental DNAs as
the template.
• Transferring the genetic information to the
descendant generation with a high fidelity
replication
parental DNA
daughter DNA
2

3. Daughter strand synthesis
• Chemical formulation:
(dNMP)n + dNTP (dNMP)n+1 + PPi
DNA strand substrate
elongated
DNA strand
• The nature of DNA replication is a
series of 3´- 5´phosphodiester bond
formation catalyzed by a group of
enzymes.
3

4. Phosphodiester bond formation
4

5. Template: double stranded DNA
Substrate: dNTP
Primer: short RNA fragment with a
free 3´-OH end
Enzyme: DNA-dependent DNA
polymerase (DDDP),
other enzymes,
protein factor
DNA replication system
5

6. Characteristics of replication
 Semi-conservative replication
 Bidirectional replication
 Semi-continuous replication
 High fidelity
6

7. §1.1 Semi-Conservative Replication
7

8. §1.2 Bidirectional Replication
• Replication starts from unwinding the
dsDNA at a particular point (called
origin), followed by the synthesis on
each strand.
• The parental dsDNA and two newly
formed dsDNA form a Y-shape
structure called replication fork.
8

9. Bidirectional replication
9
3'
5'
5'
3'
5'
3'
5'
3'
direction of
replication

10. Replication of prokaryotes
The replication
process starts
from the origin,
and proceeds
in two opposite
directions. It is
named 
replication.
10

11. 11

12. 12

13. Replication of eukaryotes
• Chromosomes of eukaryotes have
multiple origins.
• The space between two adjacent
origins is called the replicon, a
functional unit of replication.
13

14. 5'
3'
3'
5'
bidirectional replication
fusion of bubbles
3'
5'
3'
5'
5'
3'
5'
3'
origins of DNA replication (every ~150 kb)
14

15. §1.3 Semi-continuous Replication
The daughter strands on two template
strands are synthesized differently since
the replication process obeys the
principle that DNA is synthesized from
the 5´ end to the 3´end.
15

16. 5'
3'
3'
5'
5'
direction of unwinding
3'
On the template having the 3´- end, the
daughter strand is synthesized
continuously in the 5’-3’ direction. This
strand is referred to as the leading
strand.
Leading strand
16

17. Semi-continuous replication
3'
5'
5'
3'
replication direction
Okazaki fragment
3'
5'
leading strand
3'
5'
3'
5'
replication fork
17

18. • Many DNA fragments are synthesized
sequentially on the DNA template
strand having the 5´- end. These DNA
fragments are called Okazaki
fragments. They are 1000 – 2000 nt
long for prokaryotes and 150-200 nt
long for eukaryotes.
• The daughter strand consisting of
Okazaki fragments is called the
lagging strand.
Okazaki fragments
18

19. Continuous synthesis of the leading
strand and discontinuous synthesis of
the lagging strand represent a unique
feature of DNA replication. It is
referred to as the semi-continuous
replication.
Semi-continuous replication
19

20. Section 2
Enzymology
of DNA Replication

21. Enzymes and protein factors
protein Mr # function
Dna A protein 50,000 1 recognize origin
Dna B protein 300,000 6 open dsDNA
Dna C protein 29,000 1 assist Dna B binding
DNA pol Elongate the DNA
strands
Dna G protein 60,000 1 synthesize RNA primer
SSB 75,600 4 single-strand binding
DNA topoisomerase 400,000 4 release supercoil
constraint
21

22. • The first DNA-
dependent DNA
polymerase (short for
DNA-pol I) was
discovered in 1958 by
Arthur Kornberg who
received Nobel Prize in
physiology or medicine
in 1959.
§2.1 DNA Polymerase
DNA-pol of prokaryotes
22

23. • Later, DNA-pol II and DNA-pol III were
identified in experiments using
mutated E.coli cell line.
• All of them possess the following
biological activity.
1. 53 polymerizing
2. exonuclease
23

24. DNA-pol of E. coli
24

25. DNA-pol I
• Mainly
responsible for
proofreading
and filling the
gaps, repairing
DNA damage
25

26. Klenow fragment
• small fragment (323 AA): having 5´→3´
exonuclease activity
• large fragment (604 AA): called Klenow
fragment, having DNA polymerization
and 3´→5´exonuclease activity
N end C end
DNA-pol Ⅰ
26

27. DNA-pol II
• Temporary functional when DNA-pol I
and DNA-pol III are not functional
• Still capable for doing synthesis on
the damaged template
• Participating in DNA repairing
27

28. DNA-pol III
• A heterodimer enzyme composed of
ten different subunits
• Having the highest polymerization
activity (105 nt/min)
• The true enzyme responsible for the
elongation process
28

29. Structure of DNA-pol III
α： has 5´→ 3´
polymerizing activity
ε：has 3´→ 5´
exonuclease activity
and plays a key role to
ensure the replication
fidelity.
θ: maintain
heterodimer structure
29

30. 30

31. 31

32. DNA-pol of eukaryotes
DNA-pol : elongation DNA-pol III
DNA-pol : initiate replication
and synthesize primers
DnaG,
primase
DNA-pol : replication with
low fidelity
DNA-pol : polymerization in
mitochondria
DNA-pol : proofreading and
filling gap
DNA-pol I
repairing
32

33. §2.2 Primase
• Also called DnaG
• Primase is able to synthesize primers
using free NTPs as the substrate and
the ssDNA as the template.
• Primers are short RNA fragments of a
several decades of nucleotides long.
33

34. 34

35. • Primers provide free 3´-OH groups to
react with the -P atom of dNTP to
form phosphoester bonds.
• Primase, DnaB, DnaC and an origin
form a primosome complex at the
initiation phase.
35

36. §2.3 Helicase
• Also referred to as DnaB.
• It opens the double strand DNA with
consuming ATP.
• The opening process with the
assistance of DnaA and DnaC
36

37. §2.4 SSB protein
• Stand for single strand DNA binding
protein
• SSB protein maintains the DNA
template in the single strand form in
order to
• prevent the dsDNA formation;
• protect the vulnerable ssDNA from
nucleases.
37

38. §2.5 Topoisomerase
• Opening the dsDNA will create
supercoil ahead of replication forks.
• The supercoil constraint needs to be
released by topoisomerases.
38

39. 39

40. • The interconversion of topoisomers
of dsDNA is catalyzed by a
topoisomerase in a three-step
process:
• Cleavage of one or both strands
of DNA
• Passage of a segment of DNA
through this break
• Resealing of the DNA break
40

41. • Also called -protein in prokaryotes.
• It cuts a phosphoester bond on one
DNA strand, rotates the broken DNA
freely around the other strand to relax
the constraint, and reseals the cut.
Topoisomerase I (topo I)
41

42. • It is named gyrase in prokaryotes.
• It cuts phosphoester bonds on both
strands of dsDNA, releases the
supercoil constraint, and reforms the
phosphoester bonds.
• It can change dsDNA into the
negative supercoil state with
consumption of ATP.
Topoisomerase II (topo II)
42

43. 43

44. 3'
5'
5'
3'
RNAase
P
OH
3'
5'
5'
3'
DNA polymerase
P
3'
5'
5'
3'
dNTP
DNAligase
3'
5'
5'
3'
ATP
§2.6 DNA Ligase
44

45. • Connect two adjacent ssDNA strands
by joining the 3´-OH of one DNA
strand to the 5´-P of another DNA
strand.
• Sealing the nick in the process of
replication, repairing, recombination,
and splicing.
45

46. §2.7 Replication Fidelity
• Replication based on the principle of
base pairing is crucial to the high
accuracy of the genetic information
transfer.
• Enzymes use two mechanisms to
ensure the replication fidelity.
– Proofreading and real-time correction
– Base selection
46

47. • DNA-pol I has the function to correct
the mismatched nucleotides.
• It identifies the mismatched
nucleotide, removes it using the 3´-
5´ exonuclease activity, add a correct
base, and continues the replication.
Proofreading and correction
47

48. 3´→5´
exonuclease
activity
excise mismatched
nuleotides
5´→3´
exonuclease
activity
cut primer or
excise mutated
segment
C T T C A G G A
G A A G T C C G G C G
5' 3'
3' 5'
Exonuclease functions
48

49. Ensuring fidelity
• Organism survival depends on accurate genome
duplication
– A mistake in DNA replication results in a permanent
mutation in the genetic material & the possible
elimination of that cell's progeny
• 1. In E. coli, the chance of incorrect nucleotide
incorporation is <10-9; fewer than 1 out of 1 billion
nucleotides
• 2. The E. coli genome contains ~4 x 106 nucleotide
pairs, Thus, this error rate corresponds <1 nucleotide
alteration for every 100 replication cycles
DNA Replication…
49

50. • Ensuring fidelity
Infidelity is detected based on the
chemical conformation of nucleotide
pairs
– 1. DNA polymerase
discriminates among 4
different precursors as they
move in & out of active site
– 2. Only one of them forms a
proper geometric fit with the
template, producing an A-T or
G-C base pair that fits in the
enzyme active site
DNA Replication…
50

51. 51

52. 52

53. • A large conformational change occurring on a
millisecond timescale locks the correct nucleotide at
the active site but promotes release of a mismatched
nucleotide.
• The positions along the reaction coordinate that decide
the yield of the reaction are not determined by the
chemical step. Rather, the initial steps of weak
substrate binding and protein conformational transition
significantly enrich the yield of a reaction with a
correct substrate, whereas the same steps diminish the
reaction probability of an incorrect substrate. 53

54. • Ensuring fidelity
• If incoming nucleotide is correct, a conformational
change occurs in which the polymerase rotates
gripping the incoming nucleotide
• If the newly formed base pair exhibits improper
geometry, the active site cannot achieve the
conformation required for catalysis & the incorrect
nucleotide is not incorporated
• In contrast, if the base pair exhibits proper geometry,
the incoming nucleotide is covalently linked to the
end of the growing strand
• Despite this mechanism, incorrect pairings
sometimes occur (~1 time for every 105 – 106
nucleotides)
DNA Replication…
54

55. • Ensuring fidelity
• Polymerase's 3'—>5' exonuclease activity takes care
of mismatched bases
• This can happen right after misincorporation or later
on (mismatch repair)
• Thus, there are three mechanisms to ensure accurate
replication
– 1. Accurate selection of nucleotides
– 2. Immediate proofreading
– 3. Postreplicative mismatch repair
DNA Replication…
55